1. It og Sundhed Thomas Nordahl Petersen, Associate Professor
Center for Biological Sequence Analysis, DTU
Building 208, room 021
Mail:

2. Lectures and exercises
Previous:
Lectures: 915 – 12
Exercises: 13 – 16
New course program:
Lectures+Exercises: 9:00 – 12:00
Wireless network:
Written exam Dec 20, bring computer, books and notes
4 hour written
Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.

3. Teachers
Thomas Nordahl Petersen
Henrik Nielsen
Anders Gorm Pedersen

4. This is a hands-on course
Lectures are giving the background/theory of a bioinformatics topic
The exercises are giving you a hands-on experience the that topic
Example
Theory of sequence alignment
Alignment by hand, filling out scoring matrices
Learning about the amino acids
Building amino acids by hand (Model building)

5. Everything is linked from the course programme

6. Daily teaching overview

7. Teaching material (2015) 7

8. Teaching material (new edition) 8

9. Outline of the course
Topics will cover a general introduction to bioinformatics
Evolution
DNA / Protein and amino acids
Alignment and scoring matrices
How does it work & what are the numbers
Visualization of multiple alignments
Phylogenetic trees and logo plots
Commonly used databases
Uniprot/Genbank & Genome browsers
Genotype, phenotype & SNP’s
Protein 3D-structure
Artificial neural networks
Practical use of bioinformatics tools
Sequence information and Logo plots

10. Outline of the course

11. The Amino Acids Thr (T) Phe (F) Val (V) Ala (A) His (H) Arg (R)
Ser (S)
Leu (L)
Cys (C)
Met (M)
Asp (D)
Lys (K)
Asn (N)
Ile (I)
Trp (W)
Gln (Q)
Glu (E)
Tyr (Y)
Pro (P)
Gly (G) 11

12. Automated sequencing
The major break-through of sequencing has happended through automation.
Fluorescent dyes.
Laser based scanning.
Capillary electrophoresis
Computer based base-calling and assembly.
Images:

13. Theory of evolution Charles Darwin 1809-1882
CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS
Charles Darwin

14. Phylogenetic tree

15. Sequence alignment - Blast

16. Sequence alignment - Blast

17. BLAST Exercise

18. Genome browsers - Ensembl

19. Protein 3D-structure

20. Protein 3D-structure

21. Neural Networks From knowledge to information
Protein sequence
Biological feature

22. Prediction of biological features Surface accessible
Predict surface accessible from
amino acid sequence only.

23. Logo plots

24. Logo plots

25. Logo plots
Information content, how is it calculated - what does it mean.

26. Written Exam